It has often been assumed that differential expression trends in psoriasis lesions are driven mostly by KCs, which are the majority cell type in full-thickness skin biopsies.
Second a maximum-scoring subnetwork is calculated from the previously enriched subnetwork using scores for differential expression and trends in metabolic profiles.
Although no further adaptin components exhibit highly significant differential expression, a general trend of upregulation of AP1 component in BSFs and downregulation of AP3 and AP4 was evident on the microarray [see Additional file 3] which suggests developmental regulation.
Among the BURP genes, RNA-Seq data has enabled nearly the same trend of differential expression and has confirmed that Glyma04g35130 BURP gene is over expressed in CS compared to CG.
This allowed inclusion of candidate genes that did not reach statistical significance but still showed a trend toward differential expression between the WT and Hnf6 Tg samples.
Two additional genes, APOD and KCNN3 were also significantly more abundant in semimembranosus and longissimus dorsi but had a trend for differential expression (P = 0.0718 and 0.0994, respectively) in the supraspinatus (Supplementary Table S3).
For miR-222, a trend towards differential expression was observed.
Non-significant interaction effect indicates that the sibling probe sets have the same trend of differential expression over treatments.
